Tree (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Displayable
  - - ini.trakem2.display.ZDisplayable
    - - ini.trakem2.display.Tree<T>

All Implemented Interfaces:

Paintable, VectorData

Direct Known Subclasses:

AreaTree, Treeline
```
public abstract class Tree<T>
extends ZDisplayable
implements VectorData
```
A sequence of points ordered in a set of connected branches.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`class`	`Tree.MeasurementPair`
`static class`	`Tree.MeasurePathDistance<I>`
`static class`	`Tree.MeshData` One color per vertex.
`class`	`Tree.NodePath`
`class`	`Tree.Pair`

Nested classes/interfaces inherited from class ini.trakem2.display.Displayable
Displayable.DataPackage, Displayable.DoEdit, Displayable.DoEdits, Displayable.DoTransforms, Displayable.SliderListener

Field Summary

Fields
Modifier and Type Field and Description

protected Set<Node<T>> end_nodes

protected Map<Layer,Set<Node<T>>> node_layer_map

protected Node<T> root
- Fields inherited from class ini.trakem2.display.ZDisplayable
  layer_set
- Fields inherited from class ini.trakem2.display.Displayable
  alpha, annotation, at, color, COMPOSITE_ADD, COMPOSITE_COLOR_YCBCR, COMPOSITE_DIFFERENCE, COMPOSITE_MULTIPLY, COMPOSITE_NORMAL, COMPOSITE_SUBTRACT, compositeModes, height, hs_linked, last_color, layer, linked_props, linked_props_origins, locked, props, TAG_ATTR1, TAG_ATTR2, title, visible, width
- Fields inherited from class ini.trakem2.persistence.DBObject
  id, project

Fields
Modifier and Type	Field and Description
`protected Set<Node<T>>`	`end_nodes`
`protected Map<Layer,Set<Node<T>>>`	`node_layer_map`
`protected Node<T>`	`root`

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`Tree(Project project, long id, HashMap<String,String> ht_attr, HashMap<Displayable,String> ht_links)` Reconstruct from XML.
`protected`	`Tree(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)` For cloning purposes, does not call addToDatabase(), neither creates any root node.
`protected`	`Tree(Project project, String title)`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`boolean`	`addNode(Node<T> parent, Node<T> child, byte confidence)` Will call calculateBoundingBox and repaint.
`protected void`	`addToLinkLater(Node<T> nd)`
`protected Node<T>`	`adjustEdgeConfidence(int inc, float x, float y, Layer layer, DisplayCanvas dc)` Expects world coordinates.
`protected boolean`	`adjustNodeColors(Node<T> nd)`
`boolean`	`apply(Layer la, Area roi, CoordinateTransform ict)` Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity).
`boolean`	`apply(VectorDataTransform vdt)`
`Point3f`	`asPoint(Node<T> nd, boolean calibrated)` Return the `Node` as a point in space.
`HashMap<Node<T>,Vertex<Node<T>>>`	`asVertices()` Return a representation of this Tree with Vertex instead of Node.
`protected void`	`cacheSubtree(Iterable<Node<T>> nodes)`
`boolean`	`calculateBoundingBox(Layer la)`
`boolean`	`canJoin(List<? extends Tree<T>> ts)` Check if it is possible to join all given Trees into this, by using the first one as the receiver (which should be this), and all the others as the ones to be merged into the receiver.
`protected void`	`clearCache()`
`protected void`	`clearState()`
`void`	`colorizeByBranchBetweennessCentrality(int etching_multiplier)`
`void`	`colorizeByNodeBetweennessCentrality()`
`HashMap<Node<T>,Integer>`	`computeAllDegrees()`
`HashMap<Node<T>,Float>`	`computeCentrality()` Computes betweenness centrality of each node in the tree, using Ulrik Brandes betweenness centrality algorithm.
`boolean`	`contains(Layer layer, double x, double y)` Returns true if the given point falls within a certain distance of any of the treeline segments, where a segment is defined as the line between a clicked point and the next.
`static <A extends Tree<?>,B extends Node<?>> A`	`copyAs(Tree<?> src, Class<A> tree_class, Class<B> node_class)` Can copy a Treeline to an AreaTree and viceversa.
`protected Coordinate<Node<T>>`	`createCoordinate(Node<T> nd)`
`protected abstract Tree.MeasurementPair`	`createMeasurementPair(Tree.NodePath np)`
`Future<JFrame>`	`createMultiTableView()` Create a GUI to list, in three tabs: starting point, branch points, end points, and all points.
`protected Node<T>`	`createNewNode(float lx, float ly, Layer layer, Node<?> modelNode)` Create a new node, copying some properties from the modelNode such as radius or color.
`void`	`createReviewStack(Node<T> first, Node<T> last, Tag tag, String filepath, int width, int height, double magnification, int image_type)` The behavior is undefined if @param last is not a descendant of @param first.
`boolean`	`crop(List<Layer> range)` Retain the data within the layer range, and through out all the rest.
`void`	`deselect()` Tell this Displayable that is has been deselected from a Display.
`void`	`destroy()` Release resources.
`void`	`dropAllTags()` Drop all tags from the nodes of this tree.
`static <A extends Tree<?>> Map<Tree<?>,Tree<?>>`	`duplicateAs(Collection<Displayable> col, Class<A> target)` Takes a collection of Tree instances and creates duplicate siblings of the target class.
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)` Exports to type t2_treeline.
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.
`protected abstract boolean`	`exportXMLNodeAttributes(StringBuilder indent, StringBuilder sb, Node<T> node)`
`protected abstract boolean`	`exportXMLNodeData(StringBuilder indent, StringBuilder sb, Node<T> node)`
`Node<T>`	`findClosestNode(Collection<Node<T>> nodes, float lx, float ly, double magnification)` Expects local coords; with precision depending on magnification.
`Node<T>`	`findClosestNodeW(Collection<Node<T>> nodes, float wx, float wy, double magnification)` Expects world coords; with precision depending on magnification.
`Node<T>`	`findClosestNodeW(float wx, float wy, Layer layer, double magnification)` Expects world coords; with precision depending on magnification.
`List<Connector>[]`	`findConnectors()` Returns an array of two Collection of connectors: the first one has the outgoing connectors, and the second one has the incoming connectors.
`protected Node<T>`	`findFirstIntersectingNode(Set<Node<T>> nodes, Area a)` Expects an Area in local coordinates.
`Map<Node<T>,Collection<Displayable>>`	`findIntersecting(Class<?> c)`
`protected Coordinate<Node<T>>`	`findNearAndGetNext(float x, float y, Layer layer, DisplayCanvas dc)`
`protected Coordinate<Node<T>>`	`findNearAndGetPrevious(float x, float y, Layer layer, DisplayCanvas dc)`
`Node<T>[]`	`findNearestEdge(float x_pl, float y_pl, Layer layer, double magnification)` Considering only the set of consecutive layers currently painted, find a point near an edge with accuracy depending upon magnification.
`Node<T>`	`findNearestEndNode(float lx, float ly, Layer layer)` Find the spatially closest node, in calibrated coords.
`Node<T>`	`findNearestNode(float lx, float ly, Layer layer)` Find the spatially closest node, in calibrated coords; expects local coords.
`Coordinate<Node<T>>`	`findNextBranchOrEndPoint(float x, float y, Layer layer, DisplayCanvas dc)` If the node found near x,y,layer is a branch point, returns it; otherwise the next down the chain; on reaching an end point, returns it.
`Node<T>`	`findNode(float lx, float ly, Layer layer, double magnification)` Find a node in @param layer near the local coords lx,ly, with precision depending on magnification.
`protected Node<T>`	`findNodeNear(float x, float y, Layer layer, DisplayCanvas dc)`
`protected Node<T>`	`findNodeNear(float x, float y, Layer layer, DisplayCanvas dc, boolean use_receiver_when_null)` Expects world coordinates.
`Coordinate<Node<T>>`	`findPreviousBranchOrRootPoint(float x, float y, Layer layer, DisplayCanvas dc)`
`List<Tree.NodePath>`	`findTaggedPairs(Tag upstream, Tag downstream)`
`Set<Tag>`	`findTags()` Search all nodes for unique tags and returns them.
`protected void`	`fireNodeRemoved(Node<T> nd)`
`Node<T>`	`firstIntersectingNode(Layer layer, Area area)` Expects Area in world coords.
`protected Point3f`	`fix(Point3f p, boolean calibrated, float[] f)` Expects a non-null float[] for reuse, and modifies @param p in place.
`ij.ImagePlus`	`flyThrough(Node<T> first, Node<T> last, int width, int height, double magnification, int type, String dir)` Fly-through image stack from first to last node.
`ij.ImagePlus`	`flyThroughMarked(int width, int height, double magnification, int type, String dir)` Fly-through image stack from source node to mark node.
`Bureaucrat`	`generateAllReviewStacks()`
`LinkedList<Region<Node<T>>>`	`generateRegions(Node<T> first, Node<T> last, int width, int height, double magnification)`
`Bureaucrat`	`generateReviewStackForSlab(float x, float y, Layer layer, double magnification)`
`Bureaucrat`	`generateReviewStackForSlab(Node<T> node)` Generate a review stack from the previous branch node or root, to the next branch node or end node.
`Tree.MeshData`	`generateSkeleton(double scale_, int parallels, int resample)`
`Bureaucrat`	`generateSubtreeReviewStacks(int x, int y, Layer layer, double magnification)`
`Bureaucrat`	`generateSubtreeReviewStacks(Node<T> root)`
`List<Point3f>`	`generateTriangles(double scale_, int parallels, int resample)` Deprecated.
`protected Node<T>`	`getActive()` The node currently being dragged or edited in some way.
`Area`	`getAreaAt(Layer layer)` In world coordinates.
`protected Rectangle`	`getBounds(Collection<? extends Node<T>> nodes)`
`Rectangle`	`getBounds(Rectangle tmp, Layer layer)` Will fill bounding box values into given rectangle -- only that part of this object showing in the given layer will be included in the box.
`Collection<Node<T>>`	`getBranchAndEndNodes()`
`Collection<Node<T>>`	`getBranchNodes()`
`Set<Node<T>>`	`getEndNodes()`
`Layer`	`getFirstLayer()` Returns the layer of lowest Z coordinate where this ZDisplayable has a point in.
`Coordinate<Node<T>>`	`getLastAdded()`
`Coordinate<Node<T>>`	`getLastEdited()`
`Node<T>`	`getLastVisited()`
`Collection<Long>`	`getLayerIds()` Get the list of Layer ids on which this ZDisplayable has data on.
`Collection<Layer>`	`getLayersWithData()` Override it to provide Layer pointers directly.
`Node<T>`	`getMarked()`
`Set<Node<T>>`	`getNodesAt(Layer layer)` Get a copy of the `Set` of `Node` that exist at `layer`; the `Node` instances are the originals.
`protected Set<Node<T>>`	`getNodesToPaint(Layer active_layer)`
`protected Set<Node<T>>`	`getNodesToPaint(Layer active_layer, List<Layer> color_cue_layers)`
`Point3f`	`getOriginPoint(boolean calibrated)`
`protected Rectangle`	`getPaintingBounds()`
`Node<T>`	`getRoot()`
`String`	`getShortTitle()` Sublcasses can override this method to provide a proper String, otherwise calls getTitle()
`boolean`	`insertNode(Node<T> parent, Node<T> child, Node<T> in_between, byte confidence)`
`boolean`	`intersects(Area area, double z_first, double z_last)`
`boolean`	`intersects(Layer layer, Area area)` Expects Area in world coords.
`boolean`	`intersects(Layer layer, Rectangle r)` Expects Rectangle in world coords.
`protected boolean`	`isAnyNear(Collection<Node<T>> nodes, float lx, float ly, float radius)`
`boolean`	`isDeletable()`
`protected boolean`	`isRoughlyInside(Layer layer, Rectangle box)` Fast and dirty, never returns a false negative but may return a false positive.
`protected boolean`	`isTagging()`
`boolean`	`join(List<? extends Tree<T>> ts)`
`void`	`keyPressed(KeyEvent ke)`
`protected boolean`	`layerRemoved(Layer la)` Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.
`boolean`	`linkPatches()` Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.
`boolean`	`markNear(float x, float y, Layer layer, double magnification)`
`ij.measure.ResultsTable`	`measure(ij.measure.ResultsTable rt)` Measures number of branch points and end points, and total cable length.
`double`	`measurePathDistance(Node<T> a, Node<T> b)` Measure the distance, in calibrated units, between nodes a and b of this tree.
`ij.measure.ResultsTable`	`measurePathDistance(Node<T> a, Node<T> b, ij.measure.ResultsTable rt)` Reuses @param rt unless it is null, in which case it creates a new one.
`List<Tree.MeasurementPair>`	`measureTaggedPairs(Tag upstream, Tag downstream)`
`void`	`mouseDragged(MouseEvent me, Layer la, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old)`
`void`	`mousePressed(MouseEvent me, Layer layer, int x_p, int y_p, double mag)`
`void`	`mouseReleased(MouseEvent me, Layer la, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r)`
`void`	`mouseWheelMoved(MouseWheelEvent mwe)` Does nothing unless overriden.
`protected abstract Tree<T>`	`newInstance()` Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).
`protected abstract Node<T>`	`newNode(float lx, float ly, Layer layer, Node<?> modelNode)`
`abstract Node<T>`	`newNode(HashMap<String,String> ht_attr)` To reconstruct from XML.
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> layers)`
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> layers, boolean with_arrows, boolean with_tags)`
`boolean`	`paintsAt(Layer layer)` Check if this instance will paint anything at the level of the given Layer.
`void`	`paintSnapshot(Graphics2D g, Layer layer, List<Layer> layers, Rectangle srcRect, double mag)`
`boolean`	`popNode(Node<T> node)` Remove a node only (not its subtree).
`boolean`	`remove2(boolean check)` Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.
`protected void`	`removeFromLinkLater(Node<T> nd)`
`void`	`removeNode(Node<T> node)` If the tree is a cyclic graph, it may destroy all.
`Bureaucrat`	`removeReviews()`
`void`	`repaint(boolean repaint_navigator, Layer la)` Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.
`boolean`	`reRoot(float x, float y, Layer layer, double magnification)` Reroots at the point closest to the x,y,layer_id world coordinate.
`boolean`	`reRoot(Node<T> nd)`
`protected void`	`setActive(Node<T> nd)` The node currently being dragged or edited in some way.
`protected Node<T>`	`setEdgeConfidence(byte confidence)` Find an edge near the world coords x,y,layer with precision depending upon magnification, and adjust its confidence to @param confidence.
`protected void`	`setLastAdded(Node<T> nd)`
`protected void`	`setLastEdited(Node<T> nd)`
`void`	`setLastMarked(Node<T> nd)`
`protected void`	`setLastVisited(Node<T> nd)` The node that paints in green, which is the receiver of events.
`void`	`setRoot(Node<T> new_root)` Used when reconstructing from XML.
`List<Tree<T>>`	`splitAt(Node<T> nd)`
`List<Tree<T>>`	`splitNear(float x, float y, Layer layer, double magnification)` Split the Tree into new Tree at the point closest to the x,y,layer world coordinate.
`protected Layer`	`toClosestPaintedNode(Layer active_layer, float wx, float wy, double magnification)` Also sets the last visited and the receiver node.
`boolean`	`unmark()`
`void`	`updateCache()` Update the internal `Node` cache; you want to invoke this operation after altering programmatically the `Layer` pointers of any of the `Node` of this `Tree`.
`protected void`	`updateView()`
`protected void`	`updateViewData(Node<?> node)`

Methods inherited from class ini.trakem2.display.ZDisplayable
exportDTD, getBucketable, getLayerSet, remove, setColor, setLayer, setLayerSet, setLayerSet, setVisible, softRemove, transformPoints, updateBucket, updateBucket

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, canSendTo, clone, clone, clone, commonDTDChildren, contains, displacePoints, exportSVG, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLinked, getLinked, getLinkedBox, getLinkedGroup, getLinkedProperties, getLinkedProperties, getLinkedProperty, getLinkedProperty, getMinimalBoundingBox, getNameId, getPerimeter, getPerimeter, getProperties, getProperty, getProperty, getTitle, getWidth, getX, getXMLSafeValue, getXMLSafeValue, getY, hasLinkedGroupWithinLayer, hasProperties, intersects, intersects, inverseTransformPoint, isLinked, isLinked, isLinked, isLocked, isLocked2, isOnlyLinkedTo, isOnlyLinkedTo, isOutOfRepaintingClip, isOutOfRepaintingClip, isVisible, link, link, makeAdjustPropertiesDialog, paintAsBox, paintOffscreen, preConcatenate, prePaint, preTransform, processAdjustPropertiesDialog, removeLinkedProperties, removeLinkedPropertiesFromOrigins, repaint, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAffineTransform, setAlpha, setAlpha, setAnnotation, setCompositeMode, setDimensions, setDimensions, setLayer, setLinkedProperties, setLinkedProperty, setLocation, setLocked, setProperty, setTitle, setVisible, snapTo, toString, transform, transformPoint, transformPoint, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformRectangle, translate, translate, unlink, unlink, unlinkAll, updateInDatabase, xmlError, xmlError

Methods inherited from class ini.trakem2.persistence.DBObject
addToDatabase, getId, getInfo, getProject, getUniqueIdentifier, removeFromDatabase, updateInDatabase

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

node_layer_map

protected final Map<Layer,Set<Node<T>>> node_layer_map

end_nodes
```
protected final Set<Node<T>> end_nodes
```

root
```
protected Node<T> root
```

Constructor Detail

Tree

protected Tree(Project project,
               String title)

Tree

protected Tree(Project project,
               long id,
               HashMap<String,String> ht_attr,
               HashMap<Displayable,String> ht_links)

Reconstruct from XML.

Tree

protected Tree(Project project,
               long id,
               String title,
               float width,
               float height,
               float alpha,
               boolean visible,
               Color color,
               boolean locked,
               AffineTransform at)

For cloning purposes, does not call addToDatabase(), neither creates any root node.

Method Detail

getNodesAt
```
public Set<Node<T>> getNodesAt(Layer layer)
```
Get a copy of the Set of Node that exist at layer; the Node instances are the originals. Returns an empty Set if none found.

getNodesToPaint

protected final Set<Node<T>> getNodesToPaint(Layer active_layer)

getNodesToPaint

protected final Set<Node<T>> getNodesToPaint(Layer active_layer,
                                             List<Layer> color_cue_layers)

paint

public final void paint(Graphics2D g,
                        Rectangle srcRect,
                        double magnification,
                        boolean active,
                        int channels,
                        Layer active_layer,
                        List<Layer> layers)

Specified by:: paint in interface Paintable
Overrides:: paint in class Displayable

paint

public final void paint(Graphics2D g,
                        Rectangle srcRect,
                        double magnification,
                        boolean active,
                        int channels,
                        Layer active_layer,
                        List<Layer> layers,
                        boolean with_arrows,
                        boolean with_tags)

getPaintingBounds

protected Rectangle getPaintingBounds()

getBounds
```
public Rectangle getBounds(Rectangle tmp,
                           Layer layer)
```
Description copied from class: Displayable

Will fill bounding box values into given rectangle -- only that part of this object showing in the given layer will be included in the box. If @param r is null, returns a new Rectangle; else, sets the bounds into @param r and returns it. If there aren't any bounds for this object at @param layer, returns either @param r with zero width and zero height, or a new Rectangle with zero width and zero height. Never returns null.

Overrides:

getBounds in class Displayable

getBounds

protected Rectangle getBounds(Collection<? extends Node<T>> nodes)

calculateBoundingBox
```
public boolean calculateBoundingBox(Layer la)
```
Specified by:

calculateBoundingBox in class ZDisplayable

repaint

public void repaint(boolean repaint_navigator,
                    Layer la)

Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.

intersects

public boolean intersects(Area area,
                          double z_first,
                          double z_last)

Specified by:: intersects in class ZDisplayable

getFirstLayer
```
public Layer getFirstLayer()
```
Description copied from class: ZDisplayable

Returns the layer of lowest Z coordinate where this ZDisplayable has a point in.

Specified by:

getFirstLayer in class ZDisplayable

addToLinkLater

protected final void addToLinkLater(Node<T> nd)

removeFromLinkLater

protected final void removeFromLinkLater(Node<T> nd)

linkPatches
```
public boolean linkPatches()
```
Description copied from class: ZDisplayable

Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.

Specified by:

linkPatches in class ZDisplayable

Returns:

whether the locking state changed.

newInstance
```
protected abstract Tree<T> newInstance()
```
Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).

newNode

protected abstract Node<T> newNode(float lx,
                                   float ly,
                                   Layer layer,
                                   Node<?> modelNode)

createNewNode

protected Node<T> createNewNode(float lx,
                                float ly,
                                Layer layer,
                                Node<?> modelNode)

Create a new node, copying some properties from the modelNode such as radius or color. The modelNode should be the node that will become the parent of the new node, but it doesn't have to be.

newNode

public abstract Node<T> newNode(HashMap<String,String> ht_attr)

To reconstruct from XML.

isDeletable
```
public boolean isDeletable()
```
Specified by:

isDeletable in class Displayable

exportDTD

public static void exportDTD(StringBuilder sb_header,
                             HashSet<String> hs,
                             String indent)

Exports to type t2_treeline.

exportXML
```
public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)
```
Description copied from class: Displayable

The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.

Overrides:

exportXML in class ZDisplayable

exportXMLNodeAttributes

protected abstract boolean exportXMLNodeAttributes(StringBuilder indent,
                                                   StringBuilder sb,
                                                   Node<T> node)

exportXMLNodeData

protected abstract boolean exportXMLNodeData(StringBuilder indent,
                                             StringBuilder sb,
                                             Node<T> node)

generateTriangles

@Deprecated
public List<Point3f> generateTriangles(double scale_,
                                                   int parallels,
                                                   int resample)

Deprecated.

See Also:: generateSkeleton

generateSkeleton

public Tree.MeshData generateSkeleton(double scale_,
                                      int parallels,
                                      int resample)

Returns:: a CustomLineMesh.PAIRWISE list for a LineMesh.

reRoot

public boolean reRoot(float x,
                      float y,
                      Layer layer,
                      double magnification)

Reroots at the point closest to the x,y,layer_id world coordinate.

Returns:: true on success.

reRoot
```
public boolean reRoot(Node<T> nd)
```
Parameters:

nd - A node of this Tree.

splitNear

public List<Tree<T>> splitNear(float x,
                               float y,
                               Layer layer,
                               double magnification)

Split the Tree into new Tree at the point closest to the x,y,layer world coordinate.

Returns:: null if no node was found near the x,y,layer point with precision dependent on magnification.

splitAt

public List<Tree<T>> splitAt(Node<T> nd)

Parameters:: nd - A node of this Tree.

cacheSubtree

protected void cacheSubtree(Iterable<Node<T>> nodes)

clearCache
```
protected void clearCache()
```

updateCache
```
public void updateCache()
```
Update the internal Node cache; you want to invoke this operation after altering programmatically the Layer pointers of any of the Node of this Tree.

contains
```
public boolean contains(Layer layer,
                        double x,
                        double y)
```
Returns true if the given point falls within a certain distance of any of the treeline segments, where a segment is defined as the line between a clicked point and the next.

Overrides:

contains in class Displayable

isAnyNear

protected boolean isAnyNear(Collection<Node<T>> nodes,
                            float lx,
                            float ly,
                            float radius)

getRoot
```
public Node<T> getRoot()
```

createCoordinate

protected Coordinate<Node<T>> createCoordinate(Node<T> nd)

findPreviousBranchOrRootPoint

public Coordinate<Node<T>> findPreviousBranchOrRootPoint(float x,
                                                         float y,
                                                         Layer layer,
                                                         DisplayCanvas dc)

findNextBranchOrEndPoint

public Coordinate<Node<T>> findNextBranchOrEndPoint(float x,
                                                    float y,
                                                    Layer layer,
                                                    DisplayCanvas dc)

If the node found near x,y,layer is a branch point, returns it; otherwise the next down the chain; on reaching an end point, returns it.

findNearAndGetNext

protected Coordinate<Node<T>> findNearAndGetNext(float x,
                                                 float y,
                                                 Layer layer,
                                                 DisplayCanvas dc)

findNearAndGetPrevious

protected Coordinate<Node<T>> findNearAndGetPrevious(float x,
                                                     float y,
                                                     Layer layer,
                                                     DisplayCanvas dc)

getLastEdited

public Coordinate<Node<T>> getLastEdited()

getLastAdded

public Coordinate<Node<T>> getLastAdded()

setEdgeConfidence
```
protected Node<T> setEdgeConfidence(byte confidence)
```
Find an edge near the world coords x,y,layer with precision depending upon magnification, and adjust its confidence to @param confidence.

Returns:

the node whose parent edge is altered, or null if none found.

adjustEdgeConfidence

protected Node<T> adjustEdgeConfidence(int inc,
                                       float x,
                                       float y,
                                       Layer layer,
                                       DisplayCanvas dc)

Expects world coordinates.

findNode

public Node<T> findNode(float lx,
                        float ly,
                        Layer layer,
                        double magnification)

Find a node in @param layer near the local coords lx,ly, with precision depending on magnification.

findClosestNodeW

public Node<T> findClosestNodeW(float wx,
                                float wy,
                                Layer layer,
                                double magnification)

Expects world coords; with precision depending on magnification.

findClosestNodeW

public Node<T> findClosestNodeW(Collection<Node<T>> nodes,
                                float wx,
                                float wy,
                                double magnification)

Expects world coords; with precision depending on magnification.

toClosestPaintedNode

protected Layer toClosestPaintedNode(Layer active_layer,
                                     float wx,
                                     float wy,
                                     double magnification)

Also sets the last visited and the receiver node. This is a GUI method.

findClosestNode

public Node<T> findClosestNode(Collection<Node<T>> nodes,
                               float lx,
                               float ly,
                               double magnification)

Expects local coords; with precision depending on magnification.

findNearestNode

public Node<T> findNearestNode(float lx,
                               float ly,
                               Layer layer)

Find the spatially closest node, in calibrated coords; expects local coords.

findNearestEndNode

public Node<T> findNearestEndNode(float lx,
                                  float ly,
                                  Layer layer)

Find the spatially closest node, in calibrated coords.

insertNode

public boolean insertNode(Node<T> parent,
                          Node<T> child,
                          Node<T> in_between,
                          byte confidence)

findNearestEdge
```
public Node<T>[] findNearestEdge(float x_pl,
                                 float y_pl,
                                 Layer layer,
                                 double magnification)
```
Considering only the set of consecutive layers currently painted, find a point near an edge with accuracy depending upon magnification.

Returns:

null if none of the edges is close enough, or an array of parent and child describing the edge.

addNode

public boolean addNode(Node<T> parent,
                       Node<T> child,
                       byte confidence)

Will call calculateBoundingBox and repaint.

popNode
```
public boolean popNode(Node<T> node)
```
Remove a node only (not its subtree).

Returns:

true on success. Will return false when the node has 2 or more children. The new edge confidence is that of the parent to the @param node.

removeNode
```
public void removeNode(Node<T> node)
```
If the tree is a cyclic graph, it may destroy all.

canJoin
```
public boolean canJoin(List<? extends Tree<T>> ts)
```
Check if it is possible to join all given Trees into this, by using the first one as the receiver (which should be this), and all the others as the ones to be merged into the receiver. Requires each Tree to have a non-null marked Node; otherwise, returns false.

join

public boolean join(List<? extends Tree<T>> ts)

findNodeNear

protected Node<T> findNodeNear(float x,
                               float y,
                               Layer layer,
                               DisplayCanvas dc)

findNodeNear

protected Node<T> findNodeNear(float x,
                               float y,
                               Layer layer,
                               DisplayCanvas dc,
                               boolean use_receiver_when_null)

Expects world coordinates. If no node is near x,y but there is only one node in the current Display view of the layer, then it returns that node.

markNear

public boolean markNear(float x,
                        float y,
                        Layer layer,
                        double magnification)

unmark
```
public boolean unmark()
```

setActive
```
protected void setActive(Node<T> nd)
```
The node currently being dragged or edited in some way.

getActive
```
protected Node<T> getActive()
```
The node currently being dragged or edited in some way.

setLastEdited

protected void setLastEdited(Node<T> nd)

setLastAdded

protected void setLastAdded(Node<T> nd)

setLastMarked

public void setLastMarked(Node<T> nd)

setLastVisited
```
protected void setLastVisited(Node<T> nd)
```
The node that paints in green, which is the receiver of events.

getMarked
```
public Node<T> getMarked()
```

getLastVisited
```
public Node<T> getLastVisited()
```

deselect
```
public void deselect()
```
Description copied from class: Displayable

Tell this Displayable that is has been deselected from a Display. If multiple displays have the same Displayable in their Selection, this Diplayabale is to act as if it has been deselected from all.

Overrides:

deselect in class Displayable

fireNodeRemoved

protected void fireNodeRemoved(Node<T> nd)

clearState
```
protected void clearState()
```

mousePressed

public void mousePressed(MouseEvent me,
                         Layer layer,
                         int x_p,
                         int y_p,
                         double mag)

Overrides:: mousePressed in class Displayable

mouseDragged

public void mouseDragged(MouseEvent me,
                         Layer la,
                         int x_p,
                         int y_p,
                         int x_d,
                         int y_d,
                         int x_d_old,
                         int y_d_old)

Overrides:: mouseDragged in class Displayable

mouseReleased

public void mouseReleased(MouseEvent me,
                          Layer la,
                          int x_p,
                          int y_p,
                          int x_d,
                          int y_d,
                          int x_r,
                          int y_r)

Overrides:: mouseReleased in class Displayable

isTagging
```
protected boolean isTagging()
```

keyPressed
```
public void keyPressed(KeyEvent ke)
```
Overrides:

keyPressed in class Displayable

adjustNodeColors

protected boolean adjustNodeColors(Node<T> nd)

mouseWheelMoved
```
public void mouseWheelMoved(MouseWheelEvent mwe)
```
Description copied from class: Displayable

Does nothing unless overriden.

Overrides:

mouseWheelMoved in class Displayable

setRoot
```
public void setRoot(Node<T> new_root)
```
Used when reconstructing from XML.

paintSnapshot

public void paintSnapshot(Graphics2D g,
                          Layer layer,
                          List<Layer> layers,
                          Rectangle srcRect,
                          double mag)

Overrides:: paintSnapshot in class Displayable

getEndNodes
```
public Set<Node<T>> getEndNodes()
```

flyThroughMarked

public ij.ImagePlus flyThroughMarked(int width,
                                     int height,
                                     double magnification,
                                     int type,
                                     String dir)

Fly-through image stack from source node to mark node.

Parameters:: type - is ImagePlus.GRAY8 or .COLOR_RGB

generateRegions

public LinkedList<Region<Node<T>>> generateRegions(Node<T> first,
                                                   Node<T> last,
                                                   int width,
                                                   int height,
                                                   double magnification)

flyThrough

public ij.ImagePlus flyThrough(Node<T> first,
                               Node<T> last,
                               int width,
                               int height,
                               double magnification,
                               int type,
                               String dir)

Fly-through image stack from first to last node. If first is not lower order than last, then start to last is returned.

Parameters:: type - is ImagePlus.GRAY8 or .COLOR_RGB

measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
Measures number of branch points and end points, and total cable length. Cable length is measured as: Cable length: the sum of all distances between all consecutive pairs of nodes. Lower-bound cable length: the sum of all distances between all end points to branch points, branch points to other branch points, and first branch point to root.

Overrides:

measure in class Displayable

intersects

public boolean intersects(Layer layer,
                          Rectangle r)

Expects Rectangle in world coords.

Overrides:: intersects in class Displayable

intersects

public boolean intersects(Layer layer,
                          Area area)

Expects Area in world coords.

Overrides:: intersects in class Displayable

firstIntersectingNode

public Node<T> firstIntersectingNode(Layer layer,
                                     Area area)

Expects Area in world coords.

Returns:: The first Node that intersects the area at the given layer, or null if none do.

findFirstIntersectingNode

protected Node<T> findFirstIntersectingNode(Set<Node<T>> nodes,
                                            Area a)

Expects an Area in local coordinates.

paintsAt
```
public boolean paintsAt(Layer layer)
```
Description copied from class: ZDisplayable

Check if this instance will paint anything at the level of the given Layer.

Overrides:

paintsAt in class ZDisplayable

createMultiTableView
```
public Future<JFrame> createMultiTableView()
```
Create a GUI to list, in three tabs: starting point, branch points, end points, and all points. The table has columns for X, Y, Z, data (radius or area), Layer, and tags. Double-click on a row positions the front display at that coordinate. An extra tab has a search field, to list nodes for a given typed-in (regex) tag.

updateView
```
protected void updateView()
```

updateViewData

protected void updateViewData(Node<?> node)

remove2
```
public boolean remove2(boolean check)
```
Description copied from class: Displayable

Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.

Overrides:

remove2 in class ZDisplayable

layerRemoved
```
protected boolean layerRemoved(Layer la)
```
Description copied from class: ZDisplayable

Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.

Overrides:

layerRemoved in class ZDisplayable

apply
```
public boolean apply(Layer la,
                     Area roi,
                     CoordinateTransform ict)
              throws Exception
```
Description copied from interface: VectorData

Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity). Does not consider links.

Specified by:

apply in interface VectorData

Parameters:

la - Only data at this Layer may be transformed.

roi - Only data inside this world-coordinates Area may be transformed.

ict - The transform to apply to the data that is in @param la and within @param roi.

Throws:

Exception

apply

public boolean apply(VectorDataTransform vdt)
              throws Exception

Specified by:: apply in interface VectorData
Throws:: Exception

getLayerIds
```
public Collection<Long> getLayerIds()
```
Description copied from class: ZDisplayable

Get the list of Layer ids on which this ZDisplayable has data on.

Overrides:

getLayerIds in class ZDisplayable

getLayersWithData
```
public Collection<Layer> getLayersWithData()
```
Description copied from class: Displayable

Override it to provide Layer pointers directly.

Overrides:

getLayersWithData in class Displayable

getAreaAt
```
public Area getAreaAt(Layer layer)
```
In world coordinates. Returns an empty area when there aren't any nodes in @param layer.

Overrides:

getAreaAt in class Displayable

isRoughlyInside

protected boolean isRoughlyInside(Layer layer,
                                  Rectangle box)

Fast and dirty, never returns a false negative but may return a false positive.

Overrides:: isRoughlyInside in class Displayable

crop
```
public boolean crop(List<Layer> range)
```
Retain the data within the layer range, and through out all the rest. Does NOT call calculateBoundingBox or updateBucket; that is your responsibility.

Overrides:

crop in class ZDisplayable

generateAllReviewStacks

public Bureaucrat generateAllReviewStacks()

generateSubtreeReviewStacks

public Bureaucrat generateSubtreeReviewStacks(Node<T> root)

createReviewStack

public void createReviewStack(Node<T> first,
                              Node<T> last,
                              Tag tag,
                              String filepath,
                              int width,
                              int height,
                              double magnification,
                              int image_type)

The behavior is undefined if @param last is not a descendant of @param first.

removeReviews
```
public Bureaucrat removeReviews()
```

findIntersecting

public Map<Node<T>,Collection<Displayable>> findIntersecting(Class<?> c)
                                                      throws Exception

Throws:: Exception

findConnectors
```
public List<Connector>[] findConnectors()
                                 throws Exception
```
Returns an array of two Collection of connectors: the first one has the outgoing connectors, and the second one has the incoming connectors.

Throws:

Exception

getShortTitle
```
public String getShortTitle()
```
Description copied from class: DBObject

Sublcasses can override this method to provide a proper String, otherwise calls getTitle()

Overrides:

getShortTitle in class Displayable

getOriginPoint

public Point3f getOriginPoint(boolean calibrated)

asPoint
```
public Point3f asPoint(Node<T> nd,
                       boolean calibrated)
```
Return the Node as a point in space.

Parameters:

nd - The Node to extract coordinates from.

calibrated - Whether to calibrate or not the point.

Returns:

The Point3f representing the node.

fix

protected Point3f fix(Point3f p,
                      boolean calibrated,
                      float[] f)

Expects a non-null float[] for reuse, and modifies @param p in place.

duplicateAs
```
public static <A extends Tree<?>> Map<Tree<?>,Tree<?>> duplicateAs(Collection<Displayable> col,
                                                                   Class<A> target)
                                                            throws Exception
```
Takes a collection of Tree instances and creates duplicate siblings of the target class. Will ignore any non-tree Displayable instances in the Collection. The duplicated trees are added to the ProjectTree as siblings of the originals, and to the LayerSet.

Returns:

The map of original trees vs copies in target class form.

Throws:

Exception

copyAs

public static <A extends Tree<?>,B extends Node<?>> A copyAs(Tree<?> src,
                                                             Class<A> tree_class,
                                                             Class<B> node_class)
                                                      throws Exception

Can copy a Treeline to an AreaTree and viceversa. Copies the transform, the nodes (with tags and confidence), and the color. The transparency, locked stated and links are not copied.

Throws:: Exception

generateReviewStackForSlab

public Bureaucrat generateReviewStackForSlab(float x,
                                             float y,
                                             Layer layer,
                                             double magnification)

Returns:: null if no node is near @param x, @param y

generateSubtreeReviewStacks

public Bureaucrat generateSubtreeReviewStacks(int x,
                                              int y,
                                              Layer layer,
                                              double magnification)

generateReviewStackForSlab
```
public Bureaucrat generateReviewStackForSlab(Node<T> node)
```
Generate a review stack from the previous branch node or root, to the next branch node or end node.

measurePathDistance

public ij.measure.ResultsTable measurePathDistance(Node<T> a,
                                                   Node<T> b,
                                                   ij.measure.ResultsTable rt)

Reuses @param rt unless it is null, in which case it creates a new one. Will check if both nodes belong to this tree.

Returns:: The used ResultsTable instance.

measurePathDistance

public double measurePathDistance(Node<T> a,
                                  Node<T> b)
                           throws Exception

Measure the distance, in calibrated units, between nodes a and b of this tree. Does not check if the nodes really belong to this tree.

Throws:: Exception

findTags
```
public Set<Tag> findTags()
```
Search all nodes for unique tags and returns them.

destroy
```
public void destroy()
```
Description copied from class: Displayable

Release resources.

Overrides:

destroy in class Displayable

computeAllDegrees

public HashMap<Node<T>,Integer> computeAllDegrees()

getBranchNodes

public Collection<Node<T>> getBranchNodes()

getBranchAndEndNodes

public Collection<Node<T>> getBranchAndEndNodes()

asVertices
```
public HashMap<Node<T>,Vertex<Node<T>>> asVertices()
```
Return a representation of this Tree with Vertex instead of Node.

computeCentrality
```
public HashMap<Node<T>,Float> computeCentrality()
```
Computes betweenness centrality of each node in the tree, using Ulrik Brandes betweenness centrality algorithm.

colorizeByNodeBetweennessCentrality

public void colorizeByNodeBetweennessCentrality()

colorizeByBranchBetweennessCentrality

public void colorizeByBranchBetweennessCentrality(int etching_multiplier)

createMeasurementPair

protected abstract Tree.MeasurementPair createMeasurementPair(Tree.NodePath np)

findTaggedPairs

public List<Tree.NodePath> findTaggedPairs(Tag upstream,
                                           Tag downstream)

measureTaggedPairs

public List<Tree.MeasurementPair> measureTaggedPairs(Tag upstream,
                                                     Tag downstream)

dropAllTags
```
public void dropAllTags()
```
Drop all tags from the nodes of this tree.

Class Tree<T>

Nested Class Summary

Nested classes/interfaces inherited from class ini.trakem2.display.Displayable

Field Summary

Fields inherited from class ini.trakem2.display.ZDisplayable

Fields inherited from class ini.trakem2.display.Displayable

Fields inherited from class ini.trakem2.persistence.DBObject

Constructor Summary

Method Summary

Methods inherited from class ini.trakem2.display.ZDisplayable

Methods inherited from class ini.trakem2.display.Displayable

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Field Detail

node_layer_map

end_nodes

root

Constructor Detail

Tree

Tree

Tree

Method Detail

getNodesAt

getNodesToPaint

getNodesToPaint

paint

paint

getPaintingBounds

getBounds

getBounds

calculateBoundingBox

repaint

intersects

getFirstLayer

addToLinkLater

removeFromLinkLater

linkPatches

newInstance

newNode

createNewNode

newNode

isDeletable

exportDTD

exportXML

exportXMLNodeAttributes

exportXMLNodeData

generateTriangles

generateSkeleton

reRoot

reRoot

splitNear

splitAt

cacheSubtree

clearCache

updateCache

contains

isAnyNear

getRoot

createCoordinate

findPreviousBranchOrRootPoint

findNextBranchOrEndPoint

findNearAndGetNext

findNearAndGetPrevious

getLastEdited

getLastAdded

setEdgeConfidence

adjustEdgeConfidence

findNode

findClosestNodeW

findClosestNodeW

toClosestPaintedNode

findClosestNode

findNearestNode

findNearestEndNode

insertNode

findNearestEdge

addNode

popNode

removeNode

canJoin